update:
I tried this video on LAN with 256K Outbound Bandwidth (bytes/sec) limit, and JWPlayer 5.7(http://developer.longtailvideo.com/t...fl5/player.swf), seek working fine.
not sure if the file name will cause any problem, I renamed it to video.mp4 before testing.

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No. I don't use Apache. Seeking time is ok, but the video's frame starting lagging, not smooth. i have tried to rename the file for long time ago but it's not working. Can you show me your mp4 link?

I had same problem on KVM, under OpenVZ everything was fine. Are you using any sort of virtualisation?

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I am using a VPS with 768 MB RAM. Is it the bottleneck? But another videos work correctly (after seek time, it's play normally, not lag in frame). Maybe, i don't know which virtualization software is used by my VPS provider, but it can be KVM.

got it ... I think it's bit rate / bandwidth issue.
when your bandwidth is wide enough, you can host high bit rate videos;
otherwise only low bit rate video can play smoothly.

the video itself has no problem.

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I have converted those files using VBR-2 pass method. The bit rate of each scene is high and low in a dynamic way. You mean the overall bit rate (file size) or the bit rate per second ?

I see, i have checked another videos. It show that the videos which over 26 MB is laggy, below 25 MB is ok.

But i think another issue is the frame rates of those videos. 29.97 fps, 30 pfs is better than 25 fps? And how much banwidth is enough for streaming videos with quality over 360p (480p, 720p)? I don't sure about this situation...

it's a network speed issue --- the download speed between the server and browser. if download speed slow, the video have to keep buffering to be able to play.

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I think you misunderstand me. I means everything working, buffering ok, but the video frames become unstable, slow than loading in the normal way. Please open the video by your windows media player, or sth elese and compare it 1 to 1 with the video on the browser which has been seeking time.

Thanks for your update. can you specify what's the root cause? so others can learn from your experience.

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I tested by using another softwares. The root cause is the original video's frames rate, i met 2 cases both of them has 24 fps. The 29.97 fps video is suitable for internet streaming than any others.

Then, Encoder software is the another issue with them. I usually use TMPGEnc with the preset optimize for small size but high quality (it need more computing power). Last night, i have tested by using Adobe Media Encoder with the same preset with TMPGEnc... it's end up like TMGPEnc. In some encoder for common user like AVS Video Converter, the quality of result can't be compared to 2 of above but the video end up is OK.

Maybe this is the bottneck of mp4. So, Youtube doesn't use mp4 for preset 480p of their video. I usually see the FLV.

I downloaded the original mp4 720p from Youtube. Everything is ok with Youtube.

Do i need a tool to move the medata of FLV to the start of file, like MP4? Can you suggest me? After conversation, we need to do a minor step to make our video can be streaming in Pseudo way. I have tried to download the FLV from Youtube, but i can't Pseudo streaming that FLV?